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I was enrolled in a class that was supposed to lead to A+ Certification. Durring the first week a friend called me up and said "I'm going to Frys to build a computer, wanna come?" Three hours later (including going for sushi) we had a computer complete (and a pretty nice one too). I recomend shopping a physical stores, but then that is always my habit.
Now then, the question is what you are willing to pay for. You can go out and buy a mobo with on board everything, a chip, a HD and a case for real cheap. Do you want it to be a gaming machine? Do you want it to be a speed demon under Linux? Do you want it not to sound like a jet engine? Do you want it to be compact? Do you want it to be a Be OS machine? All of these will add cost.
Building a machine capable of playing modern (or semi modern) games well is going to add a lot to the price: high end video card, faster processor.
Building a Linux speed demon is where you would want a second CPU. Windows isn't going to take advantage of it.
Building a quiet computer apeals to me a lot. I'm currently modifying my G4 (five slot) in this direction. I can highly recomend Seagate's Baracuda drives for this, or any other purpose. This doesn't add price so much as it adds restrictions on other parts.
Building a small computer is also fun. There are some great flex cases out there now. Shuttle even has an Athlon version of its case out (finaly). Most of my friends building comps are going in this direction.
And, yeah. Building for alternative OSs is going to restrict your options.
Building a faster box so it doesn't get outdated is hogwash. Know what you are going to do with it, and build to purpose you want. Three years down the line it will still server you well. On the converse, put a lot of RAM in it no matter what.